tbuckley/cabot-search huggingface dataset:
Abstract 4195: Spatially resolved single cell transcriptomic profiling in formalin-fixed paraffin-embedded (FFPE) tissues
Authors: Jiang He, Justin He, Timothy Wiggin, Rob Foreman, Renchao Chen, Nicolas Fernandez, George Emanuel
Journal: Cancer Research (2023)

Abstract Formalin-fixed paraffin-embedded (FFPE) tissues are the most widely used clinical sample types in histology and molecular diagnosis, but these samples are often challenging for single-cell transcriptomic analysis due to RNA degradation and protein crosslinking. A spatial transcriptomics technique with high detection efficiency and single molecule resolution is required in order to accurately profile the gene expression in FFPE samples in situ. Vizgen’s MERSCOPE platform, built on multiplexed error robust in situ hybridization MERFISH technology, directly profiles intact tissue’s transcriptome with subcellular spatial resolution. Here, we demonstrate the FFPE MERSCOPE workflow in tissues from 10 mouse and human samples, including archival clinical samples. In each sample, hundreds of thousands of cells were captured with &amp;gt;100 million transcript counts, generating detailed spatial transcriptomic data for the profiled genes in each sample. A comparison of FFPE and matched fresh frozen samples indicated that the FFPE workflow performs similarly in detection efficiency as compared to the fresh frozen protocol. We further demonstrated the MERSCOPE FFPE workflow is compatible with protein imaging by performing simultaneous protein-based cell boundary staining with MERFISH to accurately profile gene expression and map cell types in archival clinical human samples. Finally, we constructed a spatially resolved single cell atlas across eight major tumor types, mapped and cataloged different cell types within the tumor microenvironment and systematically characterized the gene expression among cells. This study demonstrates the potential for spatially resolved transcriptomic profiling of FFPE samples at single cell level to contribute to a wide range of biomedical research areas, including many applications to study human diseases. Citation Format: Jiang He, Justin He, Timothy Wiggin, Rob Foreman, Renchao Chen, Nicolas Fernandez, George Emanuel. Spatially resolved single cell transcriptomic profiling in formalin-fixed paraffin-embedded (FFPE) tissues. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4195.
Abstract 4145: Frizzled-4 expression enhances hepatocellular carcinoma progression, sorafenib resistance and suppresses anti-tumor CD8 T cell immunity
Authors: Jie Luo, Lanqi Gong, Yuma Yang, Qin Liu, Jiao Huang, Xiaona Fang, Xin-Yuan Guan
Journal: Cancer Research (2023)

Abstract Background: Hepatocellular carcinoma (HCC) is one of the most common and deadliest cancers. Sorafenib remains the globally accepted systemic first-line treatment for advanced HCC although acquired drug-resistance is becoming increasingly common. Hopefully, immune-checkpoint inhibitor therapy has recently revolutionized the treatment for advanced HCC that have poor response to sorafenib, but the durable response rate remains low in most patients for unknown reasons. This fuels a wave of research into the molecular mechanisms of tumor-intrinsic resistance to both chemotherapy and immune checkpoint blockade (ICB), which may provide potential systemic treatment options for advanced HCC patients. Methods and Results: RNA sequencing of sorafenib-resistant HCC cell lines was performed to identify Frizzled-4 (FZD4) as a critical gene for drug resistance that was further validated in animal models. Clinical implication of FZD4 overexpression was studied in HCC patients. Using genetic and pharmacological approaches, we found that FZD4 was sufficient to increase clonogenicity, migration and invasion, and prevent sorafenib-induced apoptosis. In addition, FZD4 could reduce secretion of tumor necrosis factor-alpha (TNF-α) and interferon-gamma (IFN-γ), as well as intracellular levels of cytotoxic granzyme A and perforin in CD8+ T cells, indicating significant suppression of CD8+ T cell-mediated antitumor immunity in HCC tumors. In vivo studies also revealed that FZD4 expression promoted tumorigenesis and accelerated HCC cell metastatic lung colonization. Combination therapy of FZD4 inhibitor FzM1 with sorafenib in HCC of MYC/sgp53-induced model showed a tendency to significantly impede tumor growth and improve mice survival. Moreover, gene set enrichment analysis (GSEA) identified the cholesterol homeostasis and fatty acid metabolism signaling signatures as the top activated pathways in FZD4-high HCC cells. This evidence suggests a crucial role of FZD4-involved lipid metabolism linked to the development of therapeutic resistance. Conclusion: Our study demonstrates that FZD4 expression plays a pivotal role in HCC progression and holds the potential for expanding the scope of targeted/ICB therapies to tumors that are currently unresponsive, especially in advanced HCC. The resistance mechanisms will be addressed in further work. Citation Format: Jie Luo, Lanqi Gong, Yuma Yang, Qin Liu, Jiao Huang, Xiaona Fang, Xin-Yuan Guan. Frizzled-4 expression enhances hepatocellular carcinoma progression, sorafenib resistance and suppresses anti-tumor CD8 T cell immunity. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4145.
Abstract 2007: Evaluation of the antitumor activity of ca102l, a hyaluronic acid and lenalidomide conjugate, in multiple myeloma
Authors: Eskouhie Tchaparian, Star Lin
Journal: Cancer Research (2023)

Abstract Multiple Myeloma (MM) is a rare and incurable hematological malignancy. Despite emerging treatments, there is still an unmet medical need for novel therapeutics to target the inherent and acquired drug resistance associated with MM. CA102L is a conjugate of hyaluronic acid and an anticancer drug designed to deliver its payload, Lenalidomide (Len), to MM cells via the CD44 receptor. Lenalidomide is used as a front-line therapy in MM; The CD44 receptor is highly expressed in MM and is associated with advanced clinical stages and poor survival. In addition to the enhancement of the therapeutic efficacy of Len, a reduction in off-target toxicity is suggested. The present study was designed to evaluate the efficacy of CA102L in MM and identify its potential mechanism of action. The antitumor efficacy of CA102L was tested (in vitro and in vivo) in two MM cancer models, IM-9 and NCI-H929. Protein expression was used to identify the potential targets of CA102L in MM. Both in in vitro and in vivo investigations, CA102L as a single agent displayed an improvement in potency in MM models. In CB-17 SCID mice bearing either IM-9 or NCI-H929 cells, tumor growth inhibition was significantly higher (P&amp;lt 0.05) in the CA102L (25 mg/kg) treated group compared to that of Len (25 mg/kg). Further, CD31 and hematoxylineosin (H&amp;E) staining of tumor sections from the IM-9 xenograft mice treated with CA102L resulted in greater antiangiogenic and antiproliferative effects compared to the other groups. Prolonged survival was also observed in CA102L monotherapy in H929 models relative to Len (56% vs 11%). Interestingly, in H929 cell viability studies, CA102L and Len at 400μM showed comparable cytotoxicity with a 60% cell growth inhibition, while superior activity was noted against IM-9-treatments (CA102L 60%, Len 20%). Western blot studies confirmed CRBN as the primary target of CA102L. In summary CA102L as a single agent, exhibited greater efficacy than Len in preclinical MM models, thus representing a promising potential therapeutic strategy for MM. Studies presently are ongoing to further evaluate CA102L’s preclinical profile to advance the candidate into the clinic. Citation Format: Eskouhie Tchaparian, Star Lin. Evaluation of the antitumor activity of ca102l, a hyaluronic acid and lenalidomide conjugate, in multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2007.
Abstract 1829: Generation of IL-21 INDUKINETM molecules for the treatment of cancer
Authors: Jenna M. Sullivan, Pamela A. Aderhold, Heather R. Brodkin, Kyriakos Economides, Daniel J. Hicklin, Nesreen Ismail, Yuka Lewis, Cynthia Seidel-Dugan, Cierra Spencer, William M. Winston, Andres Salmeron
Journal: Cancer Research (2023)

Abstract In the past decade, great strides have been made in the development of novel immunotherapies, such as immune checkpoint inhibitors (ICI) to treat cancer. However, despite these improvements, subsets of patients do not respond to ICI, highlighting an unmet need for alternative immunotherapies. As potent immunomodulators, cytokines have been explored as treatments for cancer but have been limited due to toxicity and poor pharmacokinetics (PK). One of these key cytokines, interleukin 21 (IL-21), is a pluripotent cytokine that activates anti-tumor T cell responses, induces B cell activation, and promotes generation and maintenance of germinal centers and tertiary lymphoid structures. A member of the common γ-chain family of cytokines, IL-21 acts on a broader range of cells than IL-2 and does not induce vascular leak syndrome. Despite being a potent inducer of immune activation, clinical activity of IL-21 has been hampered by poor PK and adverse events at dose levels associated with efficacy. To explore the potential therapeutic benefits of IL-21 as a treatment for cancer, Werewolf Therapeutics has developed different formats of IL-21 INDUKINETM polypeptides containing native human IL-21, an inactivation domain and a half-life extension domain tethered together by protease sensitive linkers. IL-21 INDUKINETM polypeptides are peripherally inactive, but due to dysregulation of the protease milieu in the tumor microenvironment, upon dosing and distribution to the tumor, the linkers are cleaved and IL-21 is released intratumorally. We will present data demonstrating that IL-21 INDUKINETM polypeptides showed in vitro and in vivo inducibility and activity. In mouse syngeneic tumor models, the IL-21 INDUKINETM polypeptides showed improved tolerability and therapeutic window compared to equal molar dosing of a half-life extended IL-21 protein (IL-21-HLE). Mechanistically, IL-21 triggered a pronounced activation of the adaptive immunity in the tumor. Efficacy in these tumor models was linked to expansion and activation of tumor infiltrating T cells, increased polyfunctionality in CD8+ T cells, as well as signs of increased activation of B cells. Together, these data support continued exploration of an IL-21 INDUKINETM polypeptide as a therapy for cancer. Citation Format: Jenna M. Sullivan, Pamela A. Aderhold, Heather R. Brodkin, Kyriakos Economides, Daniel J. Hicklin, Nesreen Ismail, Yuka Lewis, Cynthia Seidel-Dugan, Cierra Spencer, William M. Winston, Andres Salmeron. Generation of IL-21 INDUKINETM molecules for the treatment of cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1829.
Abstract 4481: Vrtx153, novel small molecule inhibitor of krasg12d
Authors: Prashant Kashinath Bhavar, Uday Kumar Surampudi, Partha Pratim Sarma, Anuj Ramesh Kshirsagar
Journal: Cancer Research (2023)

Abstract Pancreatic cancer is an intractable malignancy and is the seventh leading cause of global cancer deaths in industrialized countries and the third most common in the USA. Despite advancement in the knowledge of potential risk factors that cause pancreatic cancer and newly available tools for early diagnosis, its incidence is estimated to increase and will include 0.35 mln new cases within 2040. KRAS is the predominant isoform mutated in cancer and are found in 92-95% of Pancreatic Cancer patients, dominated by somatic mutations of KRASG12D. KRASG12D, is one of the most frequently mutated oncogenes across adenocarcinoma of Pancreas (51%), Colon and Rectal (13.4%) and Lung (3%). With KRAS mutations found in nearly all PDAC, this cancer type is arguably the most RAS-addicted cancer. KRASG12D is a clinically relevant target but owing to structural complexity of the protein, poses challenges for its effective inhibition. Previously, we reported a series of compound including a proprietary tool compound VTRX144, with low nM potency in 2D (&amp;lt;25 nM). Optimized lead from VRise de-novo platform has yielded an unparallel potent, highly selective, inhibitor, namely VRTX153. VRTX153 demonstrated high-affinity for KRASG12D in a GDP-loaded KRASG12D assay, with an IC50 value of less than 2 nM and more than1500 -fold selectivity over KRASWT, KRAS mutants and other RAS proteins including HRAS &amp; NRAS. VRTX153 inhibited ERK1/2 phosphorylation (pERK) and cell viability in KRASG12D-mutant cell lines in both 2D and 3D, as evaluated by CellTiter-Glo®. In-vivo translation of activity in a mouse xenograft model representing PDAC is being investigated. Citation Format: Prashant Kashinath Bhavar, Uday Kumar Surampudi, Partha Pratim Sarma, Anuj Ramesh Kshirsagar. Vrtx153, novel small molecule inhibitor of krasg12d. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4481.
Abstract 1821: Discovery of XNW21015, a novel, potent HPK1 inhibitor with excellent immune modulatory activity
Authors: Yuchuan Wu, Rui Hao, Xi Chen, Xiao Liu, Yonghua Xie, Shihua Wang, Bingquan Gao, Jichun Wen, Zhenwei Wu, Wengui Wang, Haiyang Wei, Yonghan Hu, Xiaojun Liu, Meijie Le, Jing Qiang
Journal: Cancer Research (2023)

Abstract Hematopoietic progenitor kinase 1 (HPK1), also known as MAP4K1, is a member of the STE20 family of serine/threonine kinases, and restrictedly expressed in hematopoietic cells. In T cells, HPK1 negatively regulated TCR signaling by phosphorylating the adaptor protein SLP76 on Ser376, which leads to the dissociation of the SLP-76/LAT signalosomes and downregulation of T cell priming and activation. HPK1 knockout (KO) or kinase-inactive (KI) mice spontaneously reject tumors with an enhanced immune response compared to wild-type ones. Thus, HPK1 is a novel immuno-oncology (I/O) target. In this work, we described the discovery of a potent HPK1 inhibitor starting from comprehensive SAR-based design with guidance from X-ray crystallography and computational modeling. These efforts led to identification of the potent azaindole inhibitor XNW21015, with excellent kinase selectivity and promising PK profile of low clearance and sufficient exposure for in vivo animal studies. XNW21015 dose-dependently inhibited phosphorylation of SLP76(Ser376) in vitro and in vivo in response to anti-CD3 agonist antibody, with concomitant enhancement in T cell activation. Oral administration of XNW21015 in mouse syngeneic tumor models showed favorable PK profile and robust anti-tumor activity as both single agent and in combination with immune checkpoint inhibitors. In a humanized PDX (patient-derived xenograft) model, XNW21015 enhanced tumor-infiltrated lymphocytes (TIL). In summary, we have discovered a novel, highly potent and selective HPK1 inhibitor XNW21015 as promising small molecule I/O agent, as monotherapy or in combination with immune checkpoint inhibitors. Citation Format: Yuchuan Wu, Rui Hao, Xi Chen, Xiao Liu, Yonghua Xie, Shihua Wang, Bingquan Gao, Jichun Wen, Zhenwei Wu, Wengui Wang, Haiyang Wei, Yonghan Hu, Xiaojun Liu, Meijie Le, Jing Qiang. Discovery of XNW21015, a novel, potent HPK1 inhibitor with excellent immune modulatory activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1821.
Abstract 1091: MDM2 inhibition as a novel radio-sensitizing strategy for endometrial cancer
Authors: Aaron Petty, Brian Yard, Arda Durmaz, Jacob Scott, Roberto Vargas
Journal: Cancer Research (2023)

Abstract Introduction: As opposed to other malignancies, the majority of endometrial cancer (EC) cases are wild-type for TP53. Approximately 15% of TP53-mutated EC have heterozygous mutation, preserving a fraction of wild-type signaling. Given the demonstrated impact of p53 signaling on radiotherapy (RT) response in EC, we explored the role of MDM2 inhibition as a novel radio-sensitizing strategy for EC. Methods: To assess the impact of MDM2 inhibition on cell viability and radiation response, we employed 3 parental EC cell lines of differing TP53 status (JHUEM2, Hec108, Hec1B), as well as monoclonal isolates of JHUEM2 after TP53 knockout. An intron-targeting approach facilitated TP53 cDNA complementation. Radiation response was determined by assessing cell viability with CellTiter-Glo and calculating area under the curve (AUC) with multiple dose points. Nutlin-3 and AMG-232 were both tested. All experiments were carried out in triplicate. Highest Single Agent (HSA) analysis was used to determine additive versus synergistic effects. Results: Nutlin-3 and AMG-232 were both observed to have a negative impact on cell viability, dependent on TP53 context. In the wild-type TP53 cell line (JHUEM2), IC50s for Nutlin-3 and AMG-232 were observed to be 1.417 and 0.218 μM, respectively. The heterozygous TP53-mutated cell line, Hec108, had corresponding IC50s of 6.04 and 1.10 μM. The Hec1B cell line did not exhibit a response to either drug. Subsequently, IC50 curves were calculated in the presence of multiple dose points of gamma irradiation administered as one fraction. A synergistic effect was observed with Nutlin-3 and AMG-232 in JHUEM2, while only AMG-232 reached synergy in Hec108. Conclusions: Overall, these findings nominate MDM2 inhibitors as potential radio-sensitizing strategies that would be applicable to a large proportion of EC. Given the lack of benefit from cisplatin-based radio-sensitization for recurrent EC in a recent clinical trial, this provides a novel biomarker driven strategy. Citation Format: Aaron Petty, Brian Yard, Arda Durmaz, Jacob Scott, Roberto Vargas. MDM2 inhibition as a novel radio-sensitizing strategy for endometrial cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1091.
Abstract 1251: Novel potential role of m6A-demethylase FTO (fat mass and obesity) protein in colorectal cancer
Authors: Glauben T. Landskron-Ramos, Antonia L. Domínguez-Beltrando, Mauricio Zambra-Rojas, Antonella Sanguineti, Gonzalo Vasquez, Marjorie De la Fuente, Daniela Simian, Silvana Valdebenito-Silva, Juan Saavedra, Solange Gouet, Ricardo Soto-Rifo, Daniela Sauma, Eliseo Eugenin, Mario Abedrapo, Marcela A. Hermoso, Marcela A. Hermoso
Journal: Cancer Research (2023)

Abstract Colorectal cancer (CRC) is the one of the most frequent and deadly cancer worldwide. The regulation mediated by the N6methyladenosine (m6A) demethylase protein called FTO in CRC is quite controversial. As previously studied in obesity and food intake, currently is being linked to stemness, epithelial-mesenchymal transition, chemotherapy resistance and proliferation in colon cancer cells, however, its localization and function in the tumor microenvironment (TME) and how it connects with progression remains unclear. The aim of this study was to evaluate FTO protein in tumor and healthy corresponding tissue from 22 colorectal cancer patients with different histological TNM stages (hTNM) by immunohistochemistry and multiple immunofluorescence analysis; classifying the tumor and stromal FTO localization and associating this data with clinical and histopathological features. As for content, the frequency of FTO+ cells in stromal compartments increases in more invasive stages compared to non-tumor tissue and in tumors with low desmoplasia. Regarding to localization, FTO is mostly nuclear and present in the lamina propria cells in non-tumor tissues and in immune and fibro-immune compartments in the TME, such as T cells, cancer associated fibroblasts and macrophages. In tumor cells, the percentage of FTO+ cells increase in early carcinogenic stages (hTNM I vs healthy tissue) and in moderately differentiated tumors. In addition, nuclear FTO expression increases in normal T cells and fibroblasts with a particular pattern after exposure for 24h to a colon adenocarcinoma cell-derived conditioned media, suggesting FTO activity in the TME interaction following a paracrine signal. In conclusion, the increase of the FTO protein in both tumor and stroma from CRC suggests its participation mediating TME communication. Citation Format: Glauben T. Landskron-Ramos, Antonia L. Domínguez-Beltrando, Mauricio Zambra-Rojas, Antonella Sanguineti, Gonzalo Vasquez, Marjorie De la Fuente, Daniela Simian, Silvana Valdebenito-Silva, Juan Saavedra, Solange Gouet, Ricardo Soto-Rifo, Daniela Sauma, Eliseo Eugenin, Mario Abedrapo, Marcela A. Hermoso, Marcela A. Hermoso. Novel potential role of m6A-demethylase FTO (fat mass and obesity) protein in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1251.